Supporters of radical Indonesian cleric Abu Bakar Bashir shout slogans during a protest against his arrest outside the Indonesian police headquarters in Jakarta, Indonesia Tuesday. Bashir was back in jail Monday after police said they had evidence he not only inspired Al Qaeda linked militants with his fiery sermons but helped set up a new terror cell that was plotting attacks on hotels and embassies in Indonesia's capital.

Tatan Syuflana/AP

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Bangkok, Thailand — An elite US-trained Indonesian police unit set up to combat Islamist terrorist networks is back in the spotlight after a hardline preacher, Abu Bakar Bashir, was arrested Monday and charged Wednesday with helping plan terrorist attacks.

His arrest for allegedly helping set up and support a terrorist training cell in Aceh Province could not have happened, analysts say, without years of counter-terrorism work by police unit Detachment 88. In recent months, the counterterrorism cops have killed or captured dozens of militants, including a bomber who trained in Afghanistan. The militants' alleged targets included Western embassies in Jakarta and President Susilo Bambang Yudhoyono.

But Detachment 88 has also been deployed against a different enemy: peaceful protesters in eastern Indonesia. Critics say that Indonesia has blurred the line between political dissent and extremist violence under the banner of counterterrorism, raising questions about the United States' support for allied security forces engaged in counterterrorism.

Last month, Defense Secretary Robert Gates agreed to restore ties with Indonesia’s military special forces, which were severed in the late 1990s over human rights abuses, including the disappearance of political activists. After 9/11, the US turned to Indonesia's police as an ally in fighting Islamic terrorism and in 2003 helped set up Detachment 88, but Indonesia's military has lately been pushing for a larger role in combating terrorism, too.

Past abuses

This raises alarm bells for human rights groups. On Aug. 2, on the eve of a high-profile visit to Maluku province by President Yudhoyono, police in the provincial capital Ambon arrested as many as 15 activists accused of separatist activities.

Yudhoyono had traveled to Ambon to inaugurate a government-sponsored sailing contest to promote tourism in the Banda Sea, a region that first drew European merchants in the 17th century in search of spices. Police and military personnel were deployed at the harbor where Yudhoyono appeared. “There’s a heightened level of security when the president visits,” says Josef Benedict, a campaigner in London for Amnesty International.

While Indonesian media reported that the activists were linked to a banned separatist group, known as RMS, Human Rights Watch said that the detained were merely planning to float balloons with political messages to draw attention to injustice under Indonesian rule.

Officials at Amnesty International and Human Rights Watch say that witness accounts indicate the direct role of Detachment 88 personnel in the arrests, and the rights groups warn that the arrested activists may be facing torture in custody based on the treatment meted out to activists in the past.

“The core of the problem is that Indonesia continues to prosecute political aspirations that are peacefully annunciated. These activists [in Maluku] are peacefully demonstrating,” says Phil Robertson, deputy director in Asia for Human Rights Watch.

Brig. General Tito Karnavian, the national commander of Detachment 88, denies that his officers took part in the latest arrests. “It’s not my unit. It’s the local police,” he says.

Detachment 88 has in the past arrested and allegedly tortured peaceful political protesters in Maluku. Human rights groups allege that Detachment 88 officers were involved in the arrest and torture of 22 activists in Maluku province who raised a banned independence flag in June 2007 in front of President Yudhoyono. In prison interviews, activists told rights groups that they had been beaten, whipped, and forced to crawl over hot asphalt during their pre-trial detention. All were subsequently convicted of rebellion and sentenced to long jail terms.

The US government responded in 2008 by suspended training of Detachment 88 units in Maluku, according to Paul Belmont, a spokesman for the American embassy in Jakarta. “We continued to emphasize our strong support for an open and transparent legal system to look into any claims of excessive use of force,” he wrote by e-mail.

Changing mandate

Detachment 88 was formed with US and Australian support following the 2002 Bali bombings and is credited with breaking up terror networks and hunting down wanted militants. Some of its officers are assigned to provincial police commands, such as in the Maluku islands, where Muslim-Christian tensions erupted into all-out sectarian fighting from 1999 to 2002.

Security analysts say that Indonesian officials have privately acknowledged that some Detachment 88 officers have recently been diverted from counter-terrorism to local priorities, such as investigations into illegal logging. In June, security officials announced a restructuring of the unit that would put it directly under the police chief and centralize its operations.

However, this restructuring would reportedly broaden Detachment 88’s aim to include ‘ethno-nationalism,’ a reference to separatist activity in eastern Papua province and in Maluku, where an armed Christian-based rebellion flared in the 1950s. Indonesia is sensitive to breakaway sentiment and still smarts over the loss of East Timor, which voted to secede from Indonesia in a 1999 referendum.

Ironically, Detachment 88 has attracted some criticism in Indonesia for being too lenient with detainees in terrorist cases. Muslim militants who recant have been given favorable treatment, as part of a program to de-radicalize other recruits. Police officers and prison guards often treat militants favorably in order to counter their indoctrination that Indonesian authorities are their enemy. But some of those militants released and classified as rehabilitated later rejoined terrorist networks, calling into question the program’s effectiveness.

In Papua province, on the Indonesian half of New Guinea island, Human Rights Watch has also documented cases of torture of suspects in police custody, though not involving Detachment 88. A banned separatist group, the Free Papua Movement, known as OPM, has struggled for decades in the heavily militarized and resource-rich region. Last December, police shot dead Kelly Kwalik, an OPM leader, who was accused of organizing armed attacks on a gold mine owned by US-based Freeport-McMoran.